Facebook and the end of an era...

I came across this image on Facebook recently and found it very amusing, despite the fact that I have been paying no attention to anything with "we are the 1%" mentioned.

One of the good things about this image is how true it is, regardless of the political climate. Such beautiful diversity exists out there, yet we tend to focus on those which are cute and cuddly, especially in conservation. This could be a good platform for a rant, but I am rather under the weather right now and want to talk about something else.

I've been on Facebook discussion boards for around four years now. In that time I have developed a lot of my views, shared them with others, helped people learn and refine their own views and had a good laugh, making many online friends (some of which I have met and intend to meet in real life). I found that I most enjoyed discussing evolution on those boards, which were Christian boards, making me one of the few theistic evolutionists able to engage in the science and willing to engage in the theology. There are others out there, but they generally are not so outspoken. I tended to stick to a single discussion board, occasionally branching out into others, but always returning to my main group, where I often built a bit of a reputation (generally good). Every so often I would migrate to a new board and find lots of creationists to debate with, but before long they would all disappear or keep quiet (I can't claim I didn't have a hand in that, but I can't claim I did either). Only the last group I was on seemed to have a steady influx of outspoken creationists.

Facebook has now removed those discussion boards. This looks to be the end of my time on those boards and is perhaps a good point in life to get away from them (it is rumoured they might return). It is a shame though, as I did enjoy it. It also means a lot of my old discussions are no longer archived and I can't pick up where I left off with people with whom I was discussing. Sometimes it got in the way of my life, causing me to neglect people, and, naturally, housework. I've wasted many useful hours on those boards, so I should be saying "good riddance," but I will mostly miss it. No other format appeals to me, though I do like blogging every so often.

So, goodbye Facebook discussions, it has been an interesting ride!

Hollyoaks & Geology?

For those of you who don't know, Hollyoaks is a British soap opera aimed mostly at teenagers, known for constantly having beautiful women (and apparently men). In the last few months there has been a serial killer storyline and it has been dragged on ridiculously. Still, I wanted to see how it turned out. I hadn't watched it at all last week, when the story reached its climax, so I've just watched four episodes online in my on time (despite a temperamental internet connection). So there, I admit it, I occasionally watch Hollyoaks.

I wouldn't normally admit to such things so publically, but I spotted something in the background which interested me:

Did you see it? It says "Precambrian times" on the banner in the background. If I remember correctly, it also says "the lophotrochozoa" though I am not sure why. The Precambrian loving geek in me could not help but hit print screen. I'll go to bed and reflect on my sad life now...

Rap guide to evolution?

Yep, you read correctly. There is a rap guide to evolution, enjoy:

A rant about discussion boards...

Facebook recently announced that they were shutting down discussion boards, though it seems to have not happened. When the deadline was looming I reflected back on my many years on those boards and how I was perceived. At first I was not very active, mostly observing, but before long I gained respect and even appeared to be intimidating to some. In recent months the respect seemed to decline and instead I am simply known as an argumentative know-it-all. I am clearly argumentative, or else I would not be on a discussion board, but if they met me in person those views might change, as I am shy and reserved.

What really stuck in my mind, and prompted this post, is the "know-it-all" accusation. Many have noted that I show confidence in the things I present, that I rarely if ever state that I don't know or that I might be wrong, and people find this surprising, a negative character trait even. I only wish they would read my blog! On discussion boards I mostly end up discussing the basics of evolution, those things which are beyond reasonable doubt in the scientific community, things which I have been studying for several years now. Why would I be anything other than confident in that situation? Why would I say that I don't know, when we are talking about the basics, about things I do know? I have often acknowledged that I could be wrong about evolution, but that the chances are so slim that it is not worth thinking about.

When we get into more complex aspects of evolution (try reading Darwinian Populations and Natural Selection by Peter Godfrey Smith) then my certainty steadily diminishes, I openly acknowledge that I might be wrong or that I don't know. On this blog I believe I have stated openly that I do not know whether contingency or convergence is the dominant trend in long term evolution, so I am critical of both Gould and Conway Morris. But really, anyone who has read my posts on Ediacarans should know that I prefer topics where I lack all of the knowledge, but sadly nobody on a Bible discussion board wants to talk about Ediacarans.

Ediacarans are a group where people have good ideas concerning what they are, but nobody really knows. They constantly defy classification. The small shelly fossils, which I am working on for my dissertation, are similar in this sense, though many of them can be classified. I am intending to make my career saying "we don't know, but let's try our best". That's what many palaeontologists, many scientists in any field, do. In fact, that's how science really works. Saying "I don't know" is a big part of science, as long as it motivates one to find out. So the know-it-all accusation is really unsupported, they just need to broach a subject which is not so simple and beyond doubt.

If you ever engage in such discussions, try doing what I do and stick to what you know, stick to your strengths. Mine are evolutionary biology, palaeontology, geology and theology of nature. But in sticking to those topics which favour your interests/qualifications, you risk being dismissed as an arrogant know-it-all.

The Creationist Concept of Kind

Introduction

This will not be a post about the ambiguity surrounding the term kind when used by creationists. The lack of taxonomic clarity can be largely ignored, as the philosophical ideas expressed through the term need to first be addressed. Kinds, in this post, will simply mean a discrete group of closely related organisms. I will attempt to demonstrate that the common creationist usage of kind goes beyond what Scripture teaches, being instead an interpretation of the possible meaning of the term, rather than its actual meaning. Many creationist arguments focus on this term, yet these, I hope to show, are not inherently Biblical.

What the Bible Says

Genesis 1:11-13 (emphasis mine)

Then God said, “Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds.” And it was so. 12 The land produced vegetation: plants bearing seed according to their kinds and trees bearing fruit with seed in it according to their kinds. And God saw that it was good. 13 And there was evening, and there was morning—the third day.

Genesis 1:20-23

And God said, “Let the water teem with living creatures, and let birds fly above the earth across the vault of the sky.” 21 So God created the great creatures of the sea and every living thing with which the water teems and that moves about in it, according to their kinds, and every winged bird according to its kind. And God saw that it was good. 22 God blessed them and said, “Be fruitful and increase in number and fill the water in the seas, and let the birds increase on the earth.” 23 And there was evening, and there was morning—the fifth day.

Genesis 1:24-25

And God said, “Let the land produce living creatures according to their kinds: the livestock, the creatures that move along the ground, and the wild animals, each according to its kind.” And it was so. 25 God made the wild animals according to their kinds, the livestock according to their kinds, and all the creatures that move along the ground according to their kinds. And God saw that it was good.

When we look at the term kind based on Scripture alone, there is no definition given. It seems that we can say with certainty that they could reproduce and likely also that we could group them together. Trying to interbreed separate kinds would be seen as unnatural, based on Genesis 1. Anything more than that is not invalid, but cannot claim to be wholly Scriptural. (The term is used in other places in Scripture, such as Genesis 7 and Deuteronomy 14, but in no way which adds to our understanding.)

Creationism and Essentialism

The creationist concept of kind goes beyond the ambiguity of Genesis in an attempt to make more scientifically robust claims. Kinds can vary, but new kinds cannot be produced and the separate kinds are not related. This is a form of essentialism, which, when applied to biology, claims that species are unchanging through time. Creationists now have to acknowledge that species do change, but they are considered to be either deviations or well within the essential range of the kind in question (the classic example is that dogs vary enormously, but will always have the defining characteristics of dogs). 

Essentialism is a philosophy which stems from the ideas of Plato, particularly Platonic idealism, which has been unwittingly embraced by creationists. In order to understand the implications of kind, creationists have been using what I will label an "essentialist theology of kind". This is widely considered to be the common biological understanding before Darwin's work favoured population thinking. The essentialist theology of kind is an explanation and interpretation of the Biblical term, but it must be acknowledged that it is not the only possible explanation and interpretation of kind. 

The Purpose of a Theology of Kind

A theology of kind is developed to provide a more thorough understanding of what the Bible is saying about creation. It is effectively trying to bridge a gap between our scientific knowledge and our Scriptural knowledge with regards to biological classification. It is nothing more than an interpretation, one we could almost label a hypothesis, which must be consistent with the Bible and with the scientific data. If it cannot fit them both, then it is insufficient and subject to either change or rejection for a better model. 

The essentialist theology of kind is often used improperly by creationists. It is presupposed as the only Biblically consistent explanation and instead of being tested against the scientific data, it is used to dictate it. Their definitions of kind are clearly Biblically consistent, but break down when tested against the biological data.

A Darwinian Theology of Kind?

Darwinian population thinking has replaced essentialism in our understanding of biology. Is it possible to have a Darwinian theology of kind which can replace the outdated essentialist theology of kind which creationists favour? In theory the answer should be yes, as it would clearly be consistent with the biological data. The problem is when we ask if it is consistent with the Biblical claims.

Creationists, using their essentialist thought, would reject the Darwinian understanding outright. Darwinian evolution makes claims which go contrary to their essentialist ideas, however, it is not the essentialism which is inherent in the Bible. Based on Scripture alone there is no real inconsistency between a Darwinian theology and the Biblical term kind. In evolution, organisms can be argued to be reproducing after their kind, as evolution is a branching process which does not involve organisms suddenly leaping across the evolutionary tree; such an occurrence would be evidence against the modern theory of evolution. Evolution produces a pattern of nested hierarchies, groups within groups, or, to borrow from the Bible, they can be seen as kinds within kinds. 

The following image is from a creationist website:

It shows dichotomies, with the groups diversifying, yet remaining the same kind. Turn it upside down and change some of the arbitrary details (the use of circles, for example) and you will probably be reminded of the following type of diagram:

The modern understanding of kinds as used by creationists is suspiciously similar to the Darwinian concept. The only differences really are their arbitrary distinctions of kinds and the time-scales involved. Look at the phylogenetic tree and follow a line from the bottom to the top; all the way along that line were ancestor-descendent relationships which can fit a Biblical definition of kind. 

Conclusion

The essentialist theology of kind used by creationists is not sufficient to explain the biological data and should not be considered synonymous with the Biblical use of kind. It can potentially be replaced with a Darwinian concept of kind, one which is Biblically and biologically consistent. This, however, is unnecessary. There is no need to bridge science and Scripture using a term which has no pragmatic meaning. Sticking to what Genesis says allows for both theologies of kind to be entertained, but there is no reason to embrace either, for we risk forcing those views upon the text instead of allowing it to speak for itself. With the Bible allowed to speak, it is clear that all organisms are blessed by God to reproduce, anything more and we are going beyond the book. 

Creationist dishonesty? Can't be...

I don't follow very many blogs, but amongst the ones I do follow there are a couple of creationists. I've critiqued them before and contrasted them both. If you follow this link, you will see my first critique, which was of a blog post by Daniel Mann. I don't know if he ever read my response to him, but even so, I responded to another of his posts, as you can see here. I was very blunt in one of those posts, describing his arguments as "unconvincing, sloppy, overly simplistic and readily [using] dishonest tactics."

It is Mann's blog I will be responding to yet again, as he recently wrote a post titled Commonalities Fail to Prove Common Descent. I originally intended to respond on his blog, but the format is awkward and word limits prevent one from being able to say much. He also censors comments on his blog, so this seems like the best option.

Some creationists are more of a challenge than Mann, see here, here and here for my exchanges with one such example. I don't expect Daniel to pay any attention to this, but it is here nonetheless. I should also not make comments about his character, but Mann has openly admitted that he lacks scientific understanding, yet he happily turns around and declares that the majority of biologists are wrong. His sort need to be kept quiet through education.

Commonalities Fail to Prove Common Descent?

When I first started reading his blog post, I expected to just ignore it, but he mentioned palaeontology and I felt the urge to write this. He states "They attempted to [prove evolution] with the fossil record. However, this record has stubbornly resisted efforts to conform it to evolutionary orthodoxy." This, to me, quite clearly shows that he is at least twenty years behind modern palaeontology. The rise of palaeobiology in the 70s sparked a lot of debate about the relationship between palaeontology and evolution, a debate which creationists have twisted horrifically. That debate raged for a decade or so and eventually evolutionary biologists started to really get their heads around what the fossil record really showed with regards to evolution. For the past twenty years, transitional fossils in particular have been cropping up near constantly (especially since China opened up to collection).

Mann then goes on to quote Stephen Jay Gould, using a quotation which I am sure he has been corrected on before as it is a blatant quote mine:

“The extreme rarity of transitional forms in the fossil record persists as a trade secret of palaeontology…The history of most fossil species includes two features particularly inconsistent with the idea that they gradually evolved:

1. Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking pretty much the same as when they disappear…

2. Sudden appearance. In any local area a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and ‘fully formed.’”

One of the first things to note is the age of the quotation. Gould has actually been dead for nearly ten years now, but these words of his are much older than that. Considering how much palaeontology has progressed in the last few decades, this quotation is clearly out of date. It must also be noted what Gould is talking about, as he is addressing the rarity of transitional forms at the species level, as this change happens too rapidly to be recorded geologically. However, there are some examples which even Gould and Eldredge acknowledged. Additionally, Gould wrote often about transitional forms above the species level. This quotation does not support Mann's claims at all. For a bit more detail on Gould's views, I wrote this piece about punctuated equilibria a few years ago, in which some examples of microevolution are acknowledged.

The beautiful mammalian jaw/inner ear bone transition.

He then quotes Mark Ridley in a quotation from 1981:

"No real evolutionist…uses the fossil record as evidence in favor of the theory of evolution as opposed to special creation."

Again, this is outdated, and again, it is out of context. Ridley goes on to explain the evidence which is used for evolution and even that is outdated, as he makes no real reference to the genetic data which has also become voluminous over the past couple of decades. Mann has often been accused of quote mining, even though he is simply parroting the quote mines of others, but he should surely have realised by now that it would make sense to check his sources to make sure they are saying what he thinks they are saying. 

He then quotes Gareth Nelson, in what is probably his worst misunderstanding:

"It is a mistake to believe that even one fossil species… can be demonstrated to have been ancestral to another."

I wholeheartedly agree. Nelson's point is that we have no way to test and confirm whether one fossil species was ancestral to another, but his point is not that we cannot confirm whether or not they were related. Palaeontologists these days are aware that claiming an ancestral relationship in the vast majority of cases is not scientific. Instead, you will find them pointing out that they possessed a transitional morphology and were closely related to other such forms. 

The transition from fish to amphibian. Note that these are not claims of direct ancestry.

Convergence is a problem for evolution??

Convergence between placentals and marsupials. Note that the convergences are functional.

In his post, Mann considers these to be nails in the coffin of common descent. Clearly he has not achieved this, but either way he declares that "[biologists] have sought out commonalities in other areas to support their belief in common descent." 

Mann's chosen example is an interesting one, as it allows us to explore evolution a little and was also something I had not looked into. Instead of addressing the most common lines of evidence, such as the abundant genetic data, he focusses on a morphological similarity and makes some arguments which appear to be becoming more common amongst anti-evolutionists. His chosen example is bioluminescence, but it is his how he uses it which interests me. 

The science deniers are becoming increasingly fascinated with convergent evolution. But unlike convergence enthusiast Simon Conway Morris, their fascination comes from an attempt to disprove evolution. It basically boils down to "oh look, evolutionists said similarities prove evolution, now they are saying that similarities can occur without them being closely related". There is a huge oversight going on here. Some of the best evidence for evolution comes from non-function, such as pseudogenes and retrotransposons in the genome. Instead, the commonalities Mann wants to look at are functional.

Convergent evolution occurs when function is similar or the same. Some problems have limited solutions and so we can expect that natural selection will lead to some traits occurring multiple times independently. Often the convergence is imperfect, or will have a different genetic substrate, but occasionally convergence appears to be perfect on all levels. Nature is constrained in the possible solutions available, so convergence is inevitable.

Hydrodynamic form is an excellent example, because there are very few ways in which a body can be streamlined in water. The torpedo shape is an obvious one for travelling at speed, so animals adapting to that lifestyle would be likely to stumble upon that form. That's why we can see the same basic body shape in sharks, ichthyosaurs and dolphins. When we look at them closely, we start to see some key differences, with one obvious one being how they actually move through the water. The up-down motion of the dolphin tail fluke gives away their mammalian ancestry. For my longer argument on that, see here: http://palaeobabbler.blogspot.com/2010/08/whats-that-swimming-toward-me.html

A very brief look at phylogenetics

When plotting evolutionary family trees (phylogenies) there are certain characters which need to be taken into account and there are some problems to overcome. The terms used here are synapomorphies, plesiomorphies, and homoplasy. I'll briefly look at these.

Synapomorphies: These are the derived traits, the ones which define a group. They are shared by taxa with a common ancestor which also has that trait, but whose ancestor does not have that trait. For example, feathers in birds and theropods are a synapomorphy which is shared by all in this group. Synapomorphies must be distinguished from plesiomorphies in order for cladistics to work.

Plesiomorphies: These are ancestral traits, shared by the taxa but going back to a further common ancestor. One such character for birds would be their erect gait, which is found in dinosaurs which do not belong to Theropoda. It therefore cannot be used as a defining feature of birds, as their non-avian ancestors possessed it too. 

Homoplasy: This is perhaps the most frustrating for such analyses. This basically includes any trait which is found in distantly related species but is, as Mann would call it, a "commonality". This includes convergent evolution, parallel evolution, and mimicry. Continuing the bird example, birds are warm blooded and so are mammals, but this evolved independently. These traits cannot be used for establishing phylogeny, though it is usually possibly to establish convergence as an explanation.

For more on convergent evolution, check out the Map of Life website for some amazing examples and explanations: http://www.mapoflife.org/   It is based on the work of Simon Conway Morris, who sees convergence as pointing towards God (so Christians need not think of him as having an atheistic agenda, as they are wont to do).

Biologists do not carelessly write off such similarities as convergent evolution, not without justification. Convergence is rarely precise and so can be quite obvious. Going back to dolphins and sharks, it is clear that their shape is dictated by natural constraints, so when we look at their other features it is clear that their ancestry is different. Dolphins are clearly mammals, not least due to their possession of mammary glands. The simple ability to nest dolphins within mammalia should show that convergent evolution is not just possible, but to be expected.

I will not comment on Mann's bio-luminescence example. I know little with regards to that specific adaptation and would not like to speak ignorantly. Convergent evolution, however, needs to be properly understood in order to criticise it, and no creationist seems to want to do the legwork. 

Tim Minchin on Evolution

A slight departure from some of the other videos I have posted, as this is comedy and therefore does not have to be scientifically accurate (it is tempting to use it as a platform for discussing how evolution works, such as putting emphasis on populations and not individuals, but I would rather laugh right now than be a pedant). Naturally I disagree with his views on religion, but still, these clips are hilarious and Tim Minchin is a talented comedian and musician. If you like musical comedy, including comedy aimed at musicians, check him out if you haven't already.

I would like...

Thanks to the repetition of "I want doesn't get" by an ex-girlfriend, I don't often declare that I want something any more. Instead I end up saying "I would like" or "I desire". Here is something I would very much like, the new Jurassic Park poster:

I particularly love that there are two scenes from the film in this image, which very well might have occurred at the same time.

On another note, I am half way through writing a couple of posts which I intended to put here before now, but other things came up. Stay tuned (they are creationist oriented, if that interests you).

Archaeopteryx Again (x11)

Two weeks ago I did a little blog about Archaeopteryx. It didn't say much, but if you are interested, see here. If only I had been lazy and waited two weeks to write about it, I could have done something much more exciting. Solnhofen in Germany has turned up an eleventh Archaeopteryx specimen, which is complete except for its missing head. This dinosaur might not be considered the first bird any more due to a study published this year (I could launch into a rant about the concept of a first bird, but I won't) but it is still an iconic transitional form and these fossils are potentially worth millions. Hopefully this fossil, like the other specimens, will yield some fascinating insights into this incredible period of evolutionary history.

I'm actually going to Solnhofen next year and like many others would love to find one of these. Chances of it happening? Slim to none. Ah well, one can dream...

Evolution Made Simple

I recently found this excellent video with Dr Yan of Bang Goes the Theory talking about evolution, using an excellent visual analogy for how random variations lead to diversity. He manages to show the cumulative effects of mutations (his mentor Dawkins will have loved him for that) and manages to slip in ideas about speciation (unsurprisingly allopatric) and even draws a little cladogram. There could have been more Liz Bonnin, but I think that about most programmes.




My only criticism of it is that it does not give the full picture. A lot of laymen mistakenly think that evolution is random and this video does nothing to really dispel that myth. Natural selection filters the random changes and is itself a non-random process. It is natural selection which really makes evolution work, so hopefully they will do a piece on that some time to complement this one. Otherwise, fantastic stuff.

Evolution: 'nuff said!

This picture was posted on Facebook and made so many points which I end up making repeatedly, and it did so succinctly. I may just use this over and over:

My only slight quibble would be the claim that life does not improve, though to be precise on that matter would have required a lot more text on the poster. Improvement is often subjective, and the way this poster means it is that things don't become "better" over time in the sense most of us would think. Evolution does, however, involve improvement in another way, because populations adapt to their environment and can be said to become "better fit" or "adaptively improved". This is, of course, dependent on the environment, so what is "better" or an "improvement" in one environment is not automatically so in another. Sadly all of the words we could use seem to be loaded in such a way which gives the wrong impression. A lot of what I just typed felt wrong because I know those words give the wrong idea about evolution.

Creation Beliefs Update

Back in February of 2010 I attempted to group together and classify the many creation beliefs that are found in Christianity. I thought I had covered all of the stand out beliefs, but now I need to update it. The original attempt can be seen here and still seems to stand up, though naturally it has some issues (and should not be taken as a prediction of origins).

A few months ago I stumbled across a blog which discussed a different view of creation, one which has its roots in gap theory (1.2.1 in my scheme) yet accepts evolution (putting it in 2.2). Perhaps I could formulate a complementary scheme which takes origins of views into account, but for now I will explain what this belief claims and how it fits into my current taxonomy.

I found this unusual view on Greg Boyd's blog for Christus Victor Ministries. It takes seriously the palaeontological evidence for extinction throughout the history of life yet tries to stick to a literal reading of Genesis creation. It is quite inventive, to say the least. Like other gap theorists, they see a gap between verse 1 and 2, but they additionally claim that nature was corrupted by demonic powers during this time. Elsewhere in the Bible, when creation is mentioned, some warfare symbolism can be seen and evolutionary gap theorists claim that this fits in between verses 1 and 2, a gap which also contains the creation and fall of angels. Then there was a cataclysmic judgement and a recreation (for which this view departs from the evidence).

It goes further than that, well into some fantastical scenarios. Ralph Winters claims that God set angels to oversee creation, angels which were also in training, which explains why it took so long. Some of these angels rebelled during the Cambrian period, hence why we have predation. Winters also goes on to claim that the rest of Genesis 1 is from the perspective of someone on Earth, though this appears to be a difference between him and Boyd and is not integral to their beliefs.

For more on evolution as cosmic conflict and modified/evolutionary gap theory, see these blog posts, as I cannot do justice to a view I know so little about:
http://gregboyd.blogspot.com/2007/06/back-to-drawing-board-on-gap-theory.html
http://gregboyd.blogspot.com/2007/07/ralph-winters-modified-gap-theory.html
http://www.gregboyd.org/blog/evolution-as-cosmic-warfare/
http://www.gregboyd.org/blog/more-on-evolution-as-cosmic-warfare/
http://www.gregboyd.org/blog/unclean-animals-and-the-corruption-of-creation/

So in my previous taxonomy this is clearly part of group 2.2 Christian Evolutionism, as it accepts evolution in the history of life. It seems to fit somewhere in or around 2.2.1 Weak Theistic Evolution, as it clings to a literalistic Genesis, even though it is still rather loose with it. I get the feeling that if I investigate more evangelical approaches to evolution, that 2.2.1 will develop its own subdivisions, within which this view, which I will keep calling Evolutionary Gap Theory, will fit.

It is not a view I buy at all, but I found it interesting nonetheless. It is a step up from a lot of the other creation views, but it does not accommodate the scientific evidence sufficiently. It seems the sort of view which would only be persuasive to theologians and evangelicals who have no proper grasp of evolution. But as I said, it is a step up at least.

Christians and Fossils: an overview

I posted this to Facebook as an overview which I do intend to do as a blog series here. Naturally it will be in much more detail, looking at each individual view and providing a critique. Some will be more detailed than others, as there are views which require more debunking and there are some where I know little about them. I also intend to do this as a possible book some day, though I intended to start it last year. 

This will simply be a brief look at modern Christian explanations for the fossil record. If any of these fit your view, then feel free to expand on what I write and explain why you believe it. If I have missed any, then please present the views I have missed.

Dismissive views:

1. Fossils can only tell us that something died. This sort of statement is often used in order not to address the fossil record or to dismiss any succession perceived in it.
2. Fossils are a test of faith. A view which allows for dismissal of the evidence.
3. Fossils were planted by Satan. This is similar to 2.
4. Fossils are fake. A rare view which invokes global conspiracy as the explanation.
None of the above views are serious attempts to engage with the evidence and so will not be addressed in any more detail.

Young Earth Creationist views:

The following four views are not necessarily mutually exclusive and all invoke a global flood.

1. Hydrological sorting. This is the view that the fossil record can be explained by organisms being sorted by density and other factors rather than evolution.http://creationwiki.org/Hydrological_sorting

2. Differential escape. This explanation is used to account for the increase in complexity seen in the fossil record. It posits that smarter, faster animals were able to escape the flood for longer, while all the slower, dumber animals died first, giving the illusion of evolving complexity. It also tries to explain the abundance of marine fossils.

3. Habitat sorting/ecological zonation. In this explanation, differing environments are used to explain fossils found in different strata and locations. The reason we do not find trilobites and man together is because trilobites are marine and humans are terrestrial, for example.

4. The European flood model. This is more complex than the other YEC models, as it does not propose the flood as an explanation for the whole fossil record. Instead, the pre-flood/post-flood boundary is in Carboniferous strata. The fossil record shows a succession of pre-flood organisms which died (all were marine because the land was destroyed), through organisms which proliferated during the flood, followed by the progressive filling of the Earth after the flood receded. A proponent of this view is Paul Garner.

Favourite evidences used by the YEC groups include polystrate fossils and fossil lagerstatte (areas of exceptional preservation). Proponents include Duane Gish, Henry Morris, Kent Hovind and the palaeontologist Kurt Wise.
http://www.bryancore.org/anniversary/04.pdf

Devolution:

I have included this one for a laugh. I once met a guy on a different discussion board who is trying to raise funds to start a museum which will explain the fossil record his way:

The greater ancestor explanation: The fossil record shows devolution, where ancestors were bigger and better in the past and have been progressively getting worse. Favoured evidence includes large mammal fossils from throughout the Cenozoic and large insect fossils from the Carboniferous.

Old Earth Creationist views:

1. Gap theory: This explains the fossil record by considering it as almost a separate creation, before God wiped the slate clean and started afresh with man and other animals. The fossil record is therefore the remnants of a failed creation.

2. Concordism and day-age: This view accepts the age of the Earth and instead suggests that there were many stages of creation and that Genesis matches what the fossils show. No large scale evolution was involved, just God stepping in to make created kinds.

Proponents of these views try to take the fossil record as a whole, though tend not to engage with it much. A prominent proponent is Hugh Ross.

Intelligent Design:

1. The patterns in the fossil record are real, but not explained by evolution. This is simply a rejection of evolution as an explanation for the whole fossil record. ID theorists differ in the degree to which God has stepped in during geological history.

Evidence given often includes the Cambrian explosion as a rapid source of new "information", and also examples such as whale evolution are used to claim that evolution would be too slow. Proponents include Michael Behe and Stephen Meyer.
http://www.discovery.org/a/2177

Theistic evolution views:

1. Evolution as cosmic warfare/modified gap theory: The fossil record is explained by cosmic warfare between Satan and good, corrupting the creation and causing mass mortality. It accepts a literal Genesis with a gap in Genesis 1.http://www.gregboyd.org/blog/evolution-as-cosmic-warfare/

2. Teleological evolution: Evolution is the explanation for the fossil record, but it also shows that there is an inevitable progression in complexity, which points to God. Proponents of this view, such as palaeontologist Simon Conway Morris, use palaeontological evidence of convergence in evolution as support, combined with constraints in nature. http://www.mapoflife.org/

3. Generic theistic evolution: Simply accepts evolution as the explanation for the fossil record, based on the evidence for an increase in the spread of complexity and faunal succession, along with transitional forms and other lines of fossil data.

Proponents of theistic evolution include Kenneth Miller, John Polkinghorne, and palaeontologists Bob Bakker and Mary Schweitzer.

Jurassic Park on the big screen.

A couple of nights ago I went to see Westworld with dinosaurs. By that, I mean that I went to see Jurassic Park at the cinema. I went to the 11:55pm showing, which was difficult as I got tired, but well worth it. I watch the films a couple of times a year, yet watching it on the big screen again had me spotting details which I had never noticed before, so I thought I would share some nuggets of information.

During the scene in which John Hammond makes his first appearance in the film, the big screen made it easier to read newspaper clippings decorating the trailer. On the fridge was an article titled "Space Aliens Stole My Face". As if that wasn't amusing enough, the words "Dinosaurs on Mars" could also be seen. There are some hints at proper palaeontological literature, but it is these which really catch the eye.

One of my favourite mistakes in the film stood out even more at the cinema. When Dennis Nedry is stealing the dinosaur embryos, the labels can be quite clearly seen. One of them reads "STEGASAURUS". I find it very amusing that one of the few Jurassic period dinosaurs mentioned is not spelled correctly, as it should be Stegosaurus. 


Whilst looking up images for this post, I stumbled upon more Jurassic Park trivia and found some of the casting choices interesting. Juliette Binoche was actually offered the role of Ellie Sattler, but turned it down to make the excellent Trois couleurs: Bleu, which is a shame, as I have a soft spot for Juliette. I've also often wondered why they did not get David Attenborough to narrate during the car scenes, as that would clearly be a case of sparing no expense, though it has come to my attention recently that he is not quite as well known in America and that Richard Kiley is known for his voice over there.

It was also brought to my attention recently that during the first proper dinosaur scene, where the Brachiosaurus is seen rearing up to get to higher branches, that it does not actually get any higher. Its head stays on the same level. It still looks good though, and the timing of the music is perfect.

If it were on for longer I might have gone again to see what else I can spot, though I will simply have to stick with the DVDs.

The world's most expensive steak.

I do love ribeye steak...

I'm in a fortunate position where I am making myself hungry by talking about one of my favourite foods and have a piece waiting for me in the fridge (I should have taken it out of the fridge though, as they should be cooked at room temperature so that they cook evenly). But this blog is not actually about steak, it is about that famous fossil bird, Archaeopteryx.

We should all know about Archaeopteryx as it is one of the most iconic transitional fossils, bring a very dinosaur-like bird, or bird-like dinosaur (the confusion is deliberate). Discovered just two years after Darwin had published The Origin of Species and had lamented the lack of such forms, there are now 10-12 specimens worldwide (all from Solnhofen, Germany, though) and they are much coveted, so find one and you can become a millionaire.

Old Archaeopteryx has been in the middle of some interesting debates. Thomas Huxley recognised it as a link between dinosaurs and modern birds, but then this view got ignored and thrown out until the 60s and 70s when palaeontologists started looking at it again. It is now considered to be rather obvious. It was also once claimed to be fake, by physicists and astronomers who know nothing about fossils, but the palaeontologists came back and showed them up for their idiocy (they would have been ignored, but Sir Fred Hoyle was very well known and needed silencing). This year is the 150th anniversary of its discovery and recent studies have "knocked it off its perch" as the first verifiable bird, see here.

The price of steak.

But what I find really interesting involves the Berlin specimen, the second Archaeopteryx found. It was discovered in 1874 or 1875 and has been labelled Archaeopteryx siemensii (as opposed to A. lithographica). It was discovered by a farmer, Jakob Niemeyer, who sold it to an innkeeper so that he could purchase a cow. That's right, he sold one of the most important fossils in the world in order to buy a cow. I hope that cow produced the tastiest steaks on the planet. Despite my love of steak, I would not have relinquished the fossil so easily, unless it was T-bone...

Taphonomy and Art

According to the Oxford Dictionary of Earth Sciences, taphonomy is "[the] study of the transition of all or part of an organism from the biosphere into the lithosphere (i.e. *fossilization). The term was coined by J. A. Efremov in 1940." A subdivision of taphonomy is biostratinomy, which looks at what happens between the time an organism dies and its final burial. This can involve the movement of the body, scavenging, decay, chemical effects and so on. It is no surprise then that a lot of palaeontologists study taphonomy, as it is useful in interpreting the fossils we find; if we know how they decay and what their remains look like in certain situations, then we can identify those phenomena in the fossil record and use them to interpret how the fossils looked when they were alive.

So it seems that I can justify looking at dead animals, as it helps with palaeontology, but that is not the real reason I do it. I find them poetic. I often take pictures of dead animals and find that they are capable of evoking a range of emotions. Some people find this strange, whereas others, including girls, have encouraged me to do it. Sometimes I am struck by the lack of emotion I feel; I know that I am looking at something which has lost its life, which has been killed when it could have gone on living, yet I often feel nothing (this seems to be true when I see rabbits and hedgehogs dead, yet when I see people harming them I get irate). Sometimes I honestly find them funny, which strikes me as even more morbid. But there are times where I get philosophical or emotional, especially when I see something such as a dog (being a dog owner means that the sight of a dead dog can tug the heart strings). I also find them fascinating, especially as they are occasionally animals I have not seen before.

So here are some pictures I have taken over the years, some with comments. Feel free to respond telling me what they made you think of. Have I taken death too lightly? Am I sick? Is this art? I'm dedicating this blog post to my friend Emily, whose blog can be found here.

This is one of my oldest ones, which looks even more poignant in black and white than it did in colour. I love corvids, they are amongst my favourite groups of birds. This one was on Bridlington beach, during a walk with a lady friend who encouraged my unusual photography habits (which nearly got me run over at one point). I don't think I can explain what I love about this image, it might be how broken it looks, as though it never stood a chance.

This was taken on the same holiday, at Reighton Sands, not far from Bridlington (the Yorkshire coast). I love how lifeless this one clearly is, as though it lost some spark very suddenly. I often find fish comical, but this one jumps out at me. We often do not see fish like we do other animals, as though they are not as important, but hopefully people will recognise the horrors of such things as shark-finning (see here for my post on shark-finning, with a depressing video).

Half way through writing this blog post I decided that it would be a good idea to make all of the pictures black and white. That way they look more artistic and I don't look as morbid...

I love how mangled this one looks. It is well on its way to not existing and is beginning to blend in with the assorted rocks and rubbish surrounding it. The phrase "gone but not forgotten" comes to mind in an unusual way. Thanks to my odd fascination, this bird has been immortalised, yet it will only ever be known for its appearance in death, after much decay has taken place. Whilst changing the colours on this one, I inverted them as well, producing an effect I really liked:

This is a porpoise I found dead on the beach at Cleethorpes. I say that I found it, one of my dogs actually did (Peanut is very good at finding dead things, though she likes to roll in them when she finds them). I was fascinated by this one, especially as it was not obvious what it was straight away. You could even see the vertebrae sticking out of the back of it:

Send me a message if you want to see more of the porpoise.

Earlier I said that dead dogs faze me a bit. This one did not. I'm not sure why. I took this photo, and many others, during a field trip to Spain. We were mapping the area (geological mapping) and this area became known as "dead dog bend" as it was near a bend in the road. This thing was huge and for a change I was not the only one taking pictures of it. Towards the end of the trip, 4 days later, I took another picture of it and it had changed somewhat (that's taphonomy for you):

The dog was large, but not the biggest dead animal I have photographed. Around a month before, I went on a fossil collecting trip to Saltwick Bay, Whitby, and saw this enormous dead seal. Its head appears to be buried, but the rest of it can be seen and it gave off quite the stench.

For a while after that I do not seem to have taken pictures of anything dead. It was probably due to the lack of a camera. Until my recent fieldwork (which I still have not written about). I took a few more pictures, but these are my favourites:

I have not edited the colour on this one because it is one of the goriest images. Sometimes that is the appeal with dead things, as it can satiate blood lust. This was one which I honestly found funny, despite its horrifying nature. I even put it up on Facebook with the lyrics to Michael Jackson's Thriller. Poor thing.

Last but not least is this snake, which I found dead on the road during my fieldwork. It was not the only one I found either. I wish I took a picture of it a few days before, when I first saw it, as it was much more three dimensional, whereas here it has almost blended into the road. By now this snake will have completely decayed. I love how the backbone is quite clear and the skin is still clearly that of a snake, yet it is a complete mess.

Well, this is a sample of some of my photography, more specifically my "dead things" collection. If anyone stumbles across this and wants to share their own, feel free to link me. I'd also love it if any poets could get some inspiration out of this. In this blog I have decided not to go into depth about the emotions they evoke, as I would rather let the images speak for themselves. We all experience death in so many ways, which is something to think about.

Rugby in Nature?

I like rugby. I don't follow any teams, mostly because I am lazy and cannot be bothered to keep up with it, though I do follow England during major competitions. As anyone who has not been living in a hole should know, the rugby world cup is currently being played in New Zealand and the knock-out stages begin this coming weekend. Due to the time difference I've had some early mornings in order to watch all of the England matches and even got up extra early to watch one of the Wales games (don't tell my ex this, but my second favourite team of the home nations is Wales, followed by Ireland). On Saturday, England will be playing France and will have their work cut out for them, as England are not playing to a high standard and could be outplayed by France if they play well (they haven't so far, but who knows?).

A couple of days ago I caught a bit of Life on the telly, which is a David Attenborough documentary from a couple of years ago. This particular episode was about birds and has some astonishing footage (look out for the bird which drops bones from a height in order to smash them and then devour them). The clip I want to share shows the red-billed tropicbird and frigate birds (man o' war birds). The tropicbirds have to run the gauntlet, trying to get their food back to their nests, whilst frigate birds attack them, trying to force them to let go of their prizes. It reminded me of rugby, watching players tackle each other for the ball. Obviously the differences are plentiful, as birds cannot form scrums in the air, but just watch this amazing clip:

A Creationist Misconception About Transitional Forms

Palaeontology is just the study of old bones and all we can know about them is that something died. It is surprising how many people have that view of the fossil record, with no idea that we can study the lives of many fossil organisms in a lot of detail, even able to determine their behaviour. When it comes to studying evolution using the fossil record we can learn quite a lot about what happened. The creationist misconception I intend to clear up is not the impoverished understanding I just mentioned, but the idea that in order to claim a fossil as a transitional form we must demonstrate that this particular organism reproduced and passed on its genes. This is an unreasonable request based on a misunderstanding of palaeontology.

What is a transitional form?


The public often use the term "missing link" when talking about fossils which plug a gap in our knowledge. This term is a useless tautology because a missing link is always missing by definition. Not to mention, whenever a "link" is found, that just creates two more smaller gaps which need filling. The correct term is transitional form which is used to refer to fossils which possess traits which fit them between two taxonomical groups (intermediate form is roughly synonymous with transitional form). Technically all fossils are transitional forms, but that assumes evolution and so will not pacify creationist attacks. What creationists seem to request is those transitions between major groups which grab the headlines and fortunately we have many.

One thing to keep in mind is that transitional forms should not be put in a chain of ancestor-descendent relationships. This cannot be done with the fossil record because it creates untestable hypotheses and becomes nothing more than story telling. Transitional forms should instead be thought of in terms of the traits they possess, as they indicate the latest possible time that trait could have evolved (the traits in question are shared, derived characteristics, which can get confusing when taken in isolation and with convergence taken into account). The traits should also not be expected to evolve at the same rates or in a sequential order; there can be overlapping.

So, did transitional forms reproduce?


It is safe to assume that they did and here is why.

1. Fossilisation is rare. Small populations are unlikely to be preserved in the fossil record, even just an individual. The larger the population, the more likely it is that an individual will become part of the fossil record and will be discovered by a palaeontologist. It is therefore safe to assume that a transitional form was not some atypical individual, but part of a large population.
2. Evolution functions by the spreading of genes in the gene pool of a population. Populations reproduce, so even if the individual which was preserved did not reproduce, it was part of a population which did reproduce. 
3. If, somehow it was a "freak of nature", then it is unlikely that it was physically very different to the population average as survival to adulthood would also be unlikely. 

Some transitional fossils are clearly part of a population, as numerous fossils have been found. Archaeopteryx is a key example considering its fame, as there are several fossil examples. Clearly these Archaeopteryx individuals were part of a large population and even if they did not reproduce themselves, the population contained many reproducing members. They are transitional forms which bridge the gap between non-avian dinosaurs and birds.

8 of the 9 Archaeopteryx specimens

A more recent example is Darwinopterus, a transitional pterosaur which fills the gap between the two major groups. It is known from numerous specimens which have yielded a wealth of information, providing evidence for sexual dimorphism in pterosaurs. One of the specimens has an egg preserved, showing unequivocally that they were capable of reproduction and the numbers demonstrate that it was part of a population.

The famous female Darwinopterus with egg.

Some transitional forms are, of course, represented by a single individual which is also often fragmented. A good example is the now well known Tiktaalik, which has been labelled as a "fishibian" due to its mixture of fish and amphibian traits. It is so clearly transitional that when its discoverer, Neil Shubin, took a model of it into an infant school class and asked them what they thought it was, some said it was a fish, some said a crocodile, whereas others recognised that it could be both. Only an unthinking pedant would claim that they are wrong. Only one specimen is known, but it is not the only organism which is part of the fish to amphibian transition. Whenever Tiktaalik is brought up, it makes sense to think of the other forms it fits with too, showing the evolution of key traits: 

This applies to all transitions. They should not be taken in isolation, but viewed as part of the whole evolutionary narrative, alongside the other transitional forms. Check out the evolution of whales or the early evolution of mammals, as there are numerous species known for each transition and all should be seen as part of a population in the deep past. 

Probabilities mean that it is extremely likely that transitional forms found were part of a population which involved reproduction. The individuals themselves need not have reproduced because evolution functions in populations, not a string of individuals. If a creationist demands evidence that the individual reproduced they are making a claim based on ignorance of palaeontology. 

I am a "paleontologist"

A friend linked to this video on Facebook earlier, I thought I would share:




A look through the comments sees someone lamenting that this would be considered politically incorrect due to the mention of evolution. What utter nonsense, palaeontologists study evolution, this should not be kept quiet (rant over).

Could it really be? A news round-up?

I've not done one of these for ages and it is about time I got back into the habit. I have been posting interesting news articles on my Facebook profile for a while now and could very easily have linked to them here. So here are the news items which have piqued my interest:

Jurassic Park is back!

Next month sees the release of the Jurassic Park trilogy on Blu-Ray, but before that the first Jurassic Park film will be shown as a limited run at the cinema again. On September 23rd the roar of the Tyrannosaurus will be heard throughout UK cinemas, and I will most certainly be going to see it (provided the loan is through). I remember when I first saw it, I even remember my anticipation of first seeing it. All I knew about it was that my mum's friend had seen a dinosaur film which he said was so realistic that it felt like the dinosaurs were going to burst out of the screen. I was around seven years old at the time and nothing was more exciting. I went to see it with my dad and sister, climbing up onto his knee during the famous raptors in the kitchen scene. We went to see it again, allowing me to be braver second time round. I collected every toy I could get my hands on and still own them all, hidden away in my asbestos-riddled loft. I watch the films a couple of times per year. When my ex-girlfriend suggested that we cuddle up and watch them all together, I instantly thought I was onto a winner (though sadly I was not allowed to say the lines along with the film). I could go on and on about the memories I have from this film, but instead I will just have to go watch it at the cinema again and create yet another memory. See here for an article about the re-release, including a trailer.

Dino Feathers in Amber


If you haven't heard about this, then I have to ask where you have been. I've had people talking to me about this loads, wanting to know if I had heard about it. A friend even randomly phoned me from home just to talk about it. Amber is rather good for preserving three dimensional fossils of things which would not normally be fossilised, such as soft parts. In this case numerous feathers have been preserved in amber dating back to the Late Cretaceous, a time when birds and non-avian dinosaurs lived side by side, both sporting feathers (it is a shared trait due to ancestry). These fossil feathers show an evolutionary range, from primitive feathers through to highly derived feathers which match those of modern birds. There is also yet more information on pigmentation in Mesozoic feathers, giving us more of an idea of the colouration of dinosaurs and early birds. It will soon be common knowledge that the colours of dinosaurs are not complete fantasy any more, though there is still a long way to go and a lot more to learn. See here for the BBC article on this well known discovery.

Sometimes spiders can be cool...


This is not a news item, though it was for me. I found a picture of a spider which interested me, rather than making me shudder and squirm as most do:

It also allows me to put another picture in this blog, as it was feeling a bit text heavy (despite that I am keeping the news short).

DNA regulation in the news again


Whenever I discuss evolution with people in any sort of detail I put emphasis on gene regulation. Genes code for proteins and are flanked by regions of DNA which determine where and when the gene in question will be expressed in the developing embryo. It is through changes in gene switches that you get changes in development, resulting in changes in morphology which can be as gradualistic as natural selection requires. This is how something such as the tetrapod limb has become so diverse; just think of wings, such as the wings of birds, bats and pterosaurs, as they are all variations on the same bones. Gene regulation changes have caused some bones to become longer, some shorter, some fuse, some are different shapes, some disappear entirely (though gradually). Evolution uses what is available and modifies it, often resulting in new combinations which allow for novel form and function. This information is important to our understanding of evolution, yet it gets overlooked a lot. This recent bit of news is the identification of the oldest known regulatory region in vertebrates and invertebrates, see here. Back in August a study was published looking at diversification events in vertebrates based on gene regulation, see here.

Ah, the classic conundrum involving fossils and genes

When looked at broadly the genetic data and the fossil data match up nicely, both showing that evolution is the explanation for how they appear. When we look closely, we find areas of conflict which are difficult to resolve. One of those problems has apparently just been solved (I haven't read the journal paper, so I don't know if their confidence has been justified). One of the problems is that we only have the genomes of recent organisms to study, giving us information only about the survivors. Each genome we have comes from lineages which got through every mass extinction; we lack the genetic information for those which perished. When we look at current genetic diversity it looks like the end result of diversification, because if there are six species in a genus it will look like that was the peak of diversity. The fossils, however, tell a different story. After mass extinctions there is often a boom in diversity, with large increases in the number of species, but as with any boom this then goes bust. Many of those species go extinct, so the fossils may show that those six species are what remains of a genus which once contained ten species. The genetic data would not be able to show this, yet the fossils do. Additionally, sometimes the fossil data is so poor that it can't tell us anything useful (such as when soft tissue is not preserved) so the genetic data is all we have. A new technique has been created, making up for this problem. See here.

Epigenetic changes are short-lived


Anyone who is interested in evolution must pay attention to epigenetics these days. Epigenetic changes do not involve the genome directly, but instead are changes which occur during the life of an individual which can affect how genes are regulated and expressed. I personally know little about epigenetics, so I may go wrong in talking about it. The recent study has shown that these changes are rarely lasting, so they play a small role in the variation available in evolution (though people still love to claim that Lamarck has been vindicated it seems). See here for more information. Also, keep in mind this other bit of news from earlier this year, as a study has shown that lasting evolutionary change takes around a million years to become fixed. Evolution in the short term can be rather fast, much like if you recorded your weight change throughout the day using extremely sensitive scales, as you would see clear changes with every meal and trip to the loo. If you do the same with a child you would find no trends in any discernible direction, until you stepped back and looked at the data over a long period, as you would clearly see growth. One of the difficulties in studying evolution is that gap from short-scale to long-scale is difficult to bridge.

Terra Nova!


This was announced a while ago and got me very excited. Next month will see the release of Spielberg-produced TV series Terra Nova, in which an apocalyptic future sees people travelling back to the Mesozoic to seek paradise and live without the problems which an ever-growing population have caused. I don't know about you, but this is right up my alley. Incredible locations, an apocalyptic future, and of course, dinosaurs.